Hybridization in parasites: consequences for adaptive evolution, pathogenesis and public health in a changing world

[No abstract available

Extreme Evolutionary Disparities Seen in Positive Selection across Seven Complex Diseases

Positive selection is known to occur when the environment that an organism inhabits is suddenly altered, as is the case across recent human history. Genome-wide association studies (GWASs) have successfully illuminated disease-associated variation. However, whether human evolution is heading towards or away from disease susceptibility in general remains an open question. The genetic-basis of common complex disease may partially be caused by positive selection events, which simultaneously increased fitness and susceptibility to disease. We analyze seven diseases studied by the Wellcome Trust Case Control Consortium to compare evidence for selection at every locus associated with disease. We take a large set of the most strongly associated SNPs in each GWA study in order to capture more hidden associations at the cost of introducing false positives into our analysis. We then search for signs of positive selection in this inclusive set of SNPs. There are striking differences between the seven studied diseases. We find alleles increasing susceptibility to Type 1 Diabetes (T1D), Rheumatoid Arthritis (RA), and Crohn's Disease (CD) underwent recent positive selection. There is more selection in alleles increasing, rather than decreasing, susceptibility to T1D. In the 80 SNPs most associated with T1D (p-value <7.01×10−5) showing strong signs of positive selection, 58 alleles associated with disease susceptibility show signs of positive selection, while only 22 associated with disease protection show signs of positive selection. Alleles increasing susceptibility to RA are under selection as well. In contrast, selection in SNPs associated with CD favors protective alleles. These results inform the current understanding of disease etiology, shed light on potential benefits associated with the genetic-basis of disease, and aid in the efforts to identify causal genetic factors underlying complex disease

Sequential Processing for Organic Photovoltaics: Design Rules for Morphology Control by Tailored Semi-Orthogonal Solvent Blends

© 2015 WILEY-VCH Verlag GmbH &amp; Co. KGaA, Weinheim. Design rules are presented for significantly expanding sequential processing (SqP) into previously inaccessible polymer:fullerene systems by tailoring binary solvent blends for fullerene deposition. Starting with a base solvent that has high fullerene solubility, 2-chlorophenol (2-CP), ellipsometry-based swelling experiments are used to investigate different co-solvents for the fullerene-casting solution. By tuning the Flory-Huggins χ parameter of the 2-CP/co-solvent blend, it is possible to optimally swell the polymer of interest for fullerene interdiffusion without dissolution of the polymer underlayer. In this way solar cell power conversion efficiencies are obtained for the PTB7 (poly[(4,8-bis[(2-ethylhexyl)oxy]benzo[1,2-b:4,5-b']dithiophene-2,6-diyl)(3-fluoro-2-[(2-ethylhexyl)carbonyl]thieno[3,4-b]thiophenediyl)]) and PC61BM (phenyl-C61-butyric acid methyl ester) materials combination that match those of blend-cast films. Both semicrystalline (e.g., P3HT (poly(3-hexylthiophene-2,5-diyl)) and entirely amorphous (e.g., PSDTTT (poly[(4,8-di(2-butyloxy)benzo[1,2-b:4,5-b']dithiophene-2,6-diyl)-alt-(2,5-bis(4,4'-bis(2-octyl)dithieno[3,2-b:2'3'-d]silole-2,6-diyl)thiazolo[5,4-d]thiazole)]) conjugated polymers can be processed into highly efficient photovoltaic devices using the solvent-blend SqP design rules. Grazing-incidence wide-angle x-ray diffraction experiments confirm that proper choice of the fullerene casting co-solvent yields well-ordered interdispersed bulk heterojunction (BHJ) morphologies without the need for subsequent thermal annealing or the use of trace solvent additives (e.g., diiodooctane). The results open SqP to polymer/fullerene systems that are currently incompatible with traditional methods of device fabrication, and make BHJ morphology control a more tractable problem

Contributions of Dopamine-Related Genes and Environmental Factors to Highly Sensitive Personality: A Multi-Step Neuronal System-Level Approach

Traditional behavioral genetic studies (e.g., twin, adoption studies) have shown that human personality has moderate to high heritability, but recent molecular behavioral genetic studies have failed to identify quantitative trait loci (QTL) with consistent effects. The current study adopted a multi-step approach (ANOVA followed by multiple regression and permutation) to assess the cumulative effects of multiple QTLs. Using a system-level (dopamine system) genetic approach, we investigated a personality trait deeply rooted in the nervous system (the Highly Sensitive Personality, HSP). 480 healthy Chinese college students were given the HSP scale and genotyped for 98 representative polymorphisms in all major dopamine neurotransmitter genes. In addition, two environment factors (stressful life events and parental warmth) that have been implicated for their contributions to personality development were included to investigate their relative contributions as compared to genetic factors. In Step 1, using ANOVA, we identified 10 polymorphisms that made statistically significant contributions to HSP. In Step 2, these polymorphism's main effects and interactions were assessed using multiple regression. This model accounted for 15% of the variance of HSP (p<0.001). Recent stressful life events accounted for an additional 2% of the variance. Finally, permutation analyses ascertained the probability of obtaining these findings by chance to be very low, p ranging from 0.001 to 0.006. Dividing these loci by the subsystems of dopamine synthesis, degradation/transport, receptor and modulation, we found that the modulation and receptor subsystems made the most significant contribution to HSP. The results of this study demonstrate the utility of a multi-step neuronal system-level approach in assessing genetic contributions to individual differences in human behavior. It can potentially bridge the gap between the high heritability estimates based on traditional behavioral genetics and the lack of reproducible genetic effects observed currently from molecular genetic studies

Y-Chromosome Based Evidence for Pre-Neolithic Origin of the Genetically Homogeneous but Diverse Sardinian Population: Inference for Association Scans

The island of Sardinia shows a unique high incidence of several autoimmune diseases with multifactorial inheritance, particularly type 1 diabetes and multiple sclerosis. The prior knowledge of the genetic structure of this population is fundamental to establish the optimal design for association studies in these diseases. Previous work suggested that the Sardinians are a relatively homogenous population, but some reports were contradictory and data were largely based on variants subject to selection. For an unbiased assessment of genetic structure, we studied a combination of neutral Y-chromosome variants, 21 biallelic and 8 short tandem repeats (STRs) in 930 Sardinian males. We found a high degree of interindividual variation but a homogenous distribution of the detected variability in samples from three separate regions of the island. One haplogroup, I-M26, is rare or absent outside Sardinia and is very common (0.37 frequency) throughout the island, consistent with a founder effect. A Bayesian full likelihood analysis (BATWING) indicated that the time from the most recent common ancestor (TMRCA) of I-M26, was 21.0 (16.0–25.5) thousand years ago (KYA) and that the population began to expand 14.0 (7.8–22.0) KYA. These results suggest a largely pre-Neolithic settlement of the island with little subsequent gene flow from outside populations. Consequently, Sardinia is an especially attractive venue for case-control genome wide association scans in common multifactorial diseases. Concomitantly, the high degree of interindividual variation in the current population facilitates fine mapping efforts to pinpoint the aetiologic polymorphisms

Classification of Plant Associated Bacteria Using RIF, a Computationally Derived DNA Marker

A DNA marker that distinguishes plant associated bacteria at the species level and below was derived by comparing six sequenced genomes of Xanthomonas, a genus that contains many important phytopathogens. This DNA marker comprises a portion of the dnaA replication initiation factor (RIF). Unlike the rRNA genes, dnaA is a single copy gene in the vast majority of sequenced bacterial genomes, and amplification of RIF requires genus-specific primers. In silico analysis revealed that RIF has equal or greater ability to differentiate closely related species of Xanthomonas than the widely used ribosomal intergenic spacer region (ITS). Furthermore, in a set of 263 Xanthomonas, Ralstonia and Clavibacter strains, the RIF marker was directly sequenced in both directions with a success rate approximately 16% higher than that for ITS. RIF frameworks for Xanthomonas, Ralstonia and Clavibacter were constructed using 682 reference strains representing different species, subspecies, pathovars, races, hosts and geographic regions, and contain a total of 109 different RIF sequences. RIF sequences showed subspecific groupings but did not place strains of X. campestris or X. axonopodis into currently named pathovars nor R. solanacearum strains into their respective races, confirming previous conclusions that pathovar and race designations do not necessarily reflect genetic relationships. The RIF marker also was sequenced for 24 reference strains from three genera in the Enterobacteriaceae: Pectobacterium, Pantoea and Dickeya. RIF sequences of 70 previously uncharacterized strains of Ralstonia, Clavibacter, Pectobacterium and Dickeya matched, or were similar to, those of known reference strains, illustrating the utility of the frameworks to classify bacteria below the species level and rapidly match unknown isolates to reference strains. The RIF sequence frameworks are available at the online RIF database, RIFdb, and can be queried for diagnostic purposes with RIF sequences obtained from unknown strains in both chromatogram and FASTA format

Distinct mandibular premolar crown morphology in Homo naledi and its implications for the evolution of Homo species in southern Africa

Homo naledi displays a combination of features across the skeleton not found in any other hominin taxon, which has hindered attempts to determine its placement within the hominin clade. Using geometric morphometrics, we assess the morphology of the mandibular premolars of the species at the enamel-dentine junction (EDJ). Comparing with specimens of Paranthropus, Australopithecus and Homo (n = 95), we find that the H. naledi premolars from the Dinaledi chamber consistently display a suite of traits (e.g., tall crown, well22 developed P3 and P4 metaconid, strongly developed P3 mesial marginal ridge, and a P3>P4 size relationship) that distinguish them from known hominin groups. Premolars from a second locality, the Lesedi Chamber, are consistent with this morphology. We also find that two specimens from South Africa, SK 96 (usually attributed to Paranthropus) and Stw 80 (Homo sp.), show similarities to the species, and we discuss a potential evolutionary link between H. naledi and hominins from Sterkfontein and Swartkrans

Patient empowerment in long-term conditions: development and preliminary testing of a new measure

BACKGROUND: Patient empowerment is viewed by policy makers and health care practitioners as a mechanism to help patients with long-term conditions better manage their health and achieve better outcomes. However, assessing the role of empowerment is dependent on effective measures of empowerment. Although many measures of empowerment exist, no measure has been developed specifically for patients with long-term conditions in the primary care setting. This study presents preliminary data on the development and validation of such a measure. METHODS: We conducted two empirical studies. Study one was an interview study to understand empowerment from the perspective of patients living with long-term conditions. Qualitative analysis identified dimensions of empowerment, and the qualitative data were used to generate items relating to these dimensions. Study two was a cross-sectional postal study involving patients with different types of long-term conditions recruited from general practices. The survey was conducted to test and validate our new measure of empowerment. Factor analysis and regression were performed to test scale structure, internal consistency and construct validity. RESULTS: Sixteen predominately elderly patients with different types of long-term conditions described empowerment in terms of 5 dimensions (identity, knowledge and understanding, personal control, personal decision-making, and enabling other patients). One hundred and ninety seven survey responses were received from mainly older white females, with relatively low levels of formal education, with the majority retired from paid work. Almost half of the sample reported cardiovascular, joint or diabetes long-term conditions. Factor analysis identified a three factor solution (positive attitude and sense of control, knowledge and confidence in decision making and enabling others), although the structure lacked clarity. A total empowerment score across all items showed acceptable levels of internal consistency and relationships with other measures were generally supportive of its construct validity. CONCLUSION: Initial analyses suggest that the new empowerment measure meets basic psychometric criteria. Reasons concerning the failure to confirm the hypothesized factor structure are discussed alongside further developments of the scale